Before you even go that far, I'd just orient the bike so that the lines are running uphill, from the caliper to levers, and without any "traps," give it some vigorous lever flicks and maybe some tapping on any exposed areas of the brake line.
Bubbles in the reservoirs aren't a problem, it's just a problem when the bubbles get between the master cylinder and the calipers, so if you can coax those bubbles up, you should be fine. IOW, unless something is very wrong, there shouldn't be significantly more air in the system than was there when you bought it 500 miles ago - it's just that the air is in a problematic area, now.